A War in Secret
by Justyce15
Summary: AU after Captain America: The Winter Soldier & The End of the Beginning, spoilers also. After S.H.I.E.L.D. is destroyed, Coulson and his team attempts to solve a cold case of the former Deputy Director of S.H.I.E.L.D., but things aren't as they seem, and Skye may finally figure out who her parents are.
1. Chapter 1: Cold Case

**A/N: **So I rushed to get this out before Turn, Turn, Turn aired, so there could be some spelling mistakes, obviously spoilers for Captain America: The Winter Soldier & The End of the Beginning. I hope you like it!

* * *

**A War In Secret**

**Chapter 1: Cold Case**

**The Bus,**

**50,000 Miles above Istanbul, Turkey**

**2 Days after the death of Thomas Nash,**

**2 Days after the disbanding of S.H.I.E.L.D.**

Coulson sat down in the remains of his office, 'this is worse than after the 084,' Coulson thought to himself, "We have nothing left, no weapons, no rations, no hope," Coulson said to the cracked desk.

"We have each other," Skye said in the doorway, Coulson had not seen her standing there, "We didn't have that two days ago."

* * *

**The Bus,**

**50,000 Miles above Arlington, Virginia**

**90 Minutes after the death of Thomas Nash**

**30 Minutes before the disbanding of S.H.I.E.L.D.**

"Put down the gun May!" Coulson shouted at the woman he had once believed to be friend.

"Drop it, Agent May," Skye came in from the cabin also pointing a gun at the pilot's head.

"Coulson, I can explain!" Melinda pleaded, "You have to trust me."

"No, I don't," Phil said, obviously shaken, "Now tell me the truth! Who are you talking to? The Clairvoyant?"

"NO!" May shouted, "It…"

"Spit it out, May," Skye said.

"It was a direct line to Director Fury," May said, "He wanted to know if you could figure out what that thing was."

"What the blue alien was," Coulson started lowering his gun, and Skye followed suit, "Fury doesn't know."

"No, it was gift from you know who," May said nodding at Coulson, "It was the mission he was on when he died. He thinks it was about the cargo, luckily he got the package back to the Triskelion."

"Who is you know who?" Skye asked, "Is some other super-secret S.H.I.E.L.D. legend that everybody but me knows?"

"His name was Quentin Cole," Coulson said, "May take control of the plane, get us to Istanbul as fast as you can."

"What about Ward?" Skye asked, "Do you still think he's a traitor?"

"And Jemma!" Fitz yelled from the lab, "She's still at the Hub! She could be in danger!"

"I have a favor I can use, I'll use it there," Coulson answered, "Don't worry, Fitz she'll be fine. And I need to talk to Ward."

"Boss," Fitz said staring at one of the lab computers, "We have a serious problem."

"What is it?" Skye asked cautiously, it was hard to believe that anything worse could come.

"Every S.H.I.E.L.D. secret ever was just put on line," Fitz screamed in his distinct scottish accent, "And… Oh my god."

"What is it?" Skye elbowed her way into lab, "Is it about me?"

"No, Hydra," Fitz said staring up at her, "Hydra has been growing inside S.H.I.E.L.D. since the beginning, Hydra was the Clairvoyant, alright I have a list of Hydra agents in S.H.I.E.L.D., and… Ward is not on it. Coulson, Ward's not with Hydra, he's clean!"

"And… Coulson left," Skye said matter of factly, "I don't think he heard you, Fitz figure out if anyone else on the team is on that list. I'll find Coulson."

"Yes, leave me to sort through 70 years of information," Fitz mumbled under his breath.

"Coulson, COULSON!" Skye's footsteps were heard throughout the plain, "I need to talk to you!"

"WHAT AREN'T YOU TELLING ME!" Coulson was pointing a gun at Ward, threatening to shoot him, "WHO ARE YOU WORKING FOR!?"

"I'm not working for anyone!" Ward pleaded, "I'm not trying to betray you! I'm working with you, and May and Skye, I'm working for S.H.I.E.L.D.!"

"He's telling the truth Coulson," Skye ran in, "Are you pointing a gun at him?" She was wide-eyed, "He's not working for the Clairvoyant."

"What do you mean?" Coulson turned towards her, still pointing the gun at Ward, "How do you know?"

"Hydra has been growing inside S.H.I.E.L.D. since it's founding," Skye explained, "And all of S.H.I.E.L.D.'s files secure or otherwise have just been published online. Including a list of all Hydra agents inside S.H.I.E.L.D. and Ward is not on that list, neither is May or Fitz, or even you. The whole team is clean."

"We should report to the Triskelion immediately," Coulson said, "Fury will want us to report."

"That may be a problem," Skye pulled out her phone and pulled up a video of a heli-carrier crashing into the Triskelion, "S.H.I.E.L.D.'s been shut down, we're done."

* * *

**The Bus,**

**45,000 Miles above Istanbul, Turkey,**

**2 Days after the death of Thomas Nash,**

**2 Days after the disbanding of S.H.I.E.L.D.**

"We have each other," Skye said, "We didn't have that two days ago."

"No, we didn't," Coulson said, "My top priority is finding out what that alien was, and who you're parents are. We may no longer be agents of S.H.I.E.L.D., but we're still a family, and we help our own. We will find answers Skye I promise."

"I'd recommend strapping in," May's voice rang out through the plane, "We'll be landing in Istanbul in about 5 minutes.

"I'll apologize to him, I promise," Skye said, thinking of the man that she had wronged.

5 Minutes later they had landed and surrounded the table in the center of the plane's cabin.

"Here are the details of the case," Coulson said, having Skye pull them up on the board, "Quentin Cole was the Deputy Director of S.H.I.E.L.D. before Maria Hill, he was killed in action smuggling a package back from a terrorist base, we now know the package was the blue alien in T.A.H.I.T.I., as Skye didn't find any of S.H.I.E.L.D.'s files on him, we believe Cole stored them on a remote drive outside of S.H.I.E.L.D. We believe Hydra killed him because they wanted the information, we also believe that they never found it."

"So we're looking for information that the world's greatest spy organization never found," Fitz said looking at his partner, "So we'll definitely find it."

"We do have one lead," Coulson said, "There is a man we believe has the file, and possibly Skye's parentage. But S.H.I.E.L.D. was never able to identify him, he goes by an alias and we believe he had Cole killed. He goes by the Broker."

"So now we're looking for two things the world's greatest spy agency never found," Simmons said, "I think Fitz was right, we don't really have a chance."

"We have something they didn't," Ward spoke up, "Trust, we trust each other, the last two days have proven this. We're going to find this bastard, and we will find you're parents Skye."

**NEXT: ABDUCTION**

* * *

**A/N:** Ok thanks for reading I hope you liked it, not a lot happened this chapter, but so much will happen in pretty much every other chapter. This will be a pretty long story, it's essentially a counterpart to my Arrow story, and chapter ten of that story will be posted in the next few days. So, as always, happy reading!


	2. Chapter 2: Humanity

**A/N:** Okay! I usually don't update this fast, but the positive feedback was so overwhelming I felt I had to give you something soon! So here is chapter 2 of…

* * *

**A War In Secret**

**Chapter 2: Humanity**

**Base of the Broker,**

**Location Unknown**

**3 Days after the Death of Thomas Nash,**

**3 Days after the disbanding of S.H.I.E.L.D.**

"Ward!" Skye shouted to empty darkness, "GRANT! WHERE ARE YOU!" She was tied to a chair, she wasn't gagged or blindfolded, "Where are you? Coulson? Simmons? Fitz? MAY!?"

"They can't hear you," A voice came out of the darkness, "Only I can."

"Who are you?" Skye, for the first time in years, was willing to admit that she was terrified.

"Oh, I am the Broker."

* * *

**The Hub,**

**Location Classified (Well actually unknown),**

**3 Hours after the death of Thomas Nash,**

**1 Hour after the disbanding of S.H.I.E.L.D.**

"Ma'am," An agent of S.H.I.E.L.D. stepped up to Victoria Hand, "The Hub has been invaded by Hydra, what are your orders?"

"Move all classified data to the Vault," Agent Hand directed the remaining agents, "We can't let Hydra get their hands-"

"That won't be a problem," Coulson suddenly appeared on the screen in the ops room, "All S.H.I.E.L.D. and Hydra information has been leaked to the web, nothing is classified anymore."

"Evacuate the Hub, and prepare to blow this station to kingdom come," Hand ordered, "Whether or not Hydra has the information, we can't let them get their hands on the Hub's arsenal."

"Victoria," Coulson said, beginning his request, "I think we can both agree you owe me for the fiasco in South Ossetia."

"What do you want, Phil?" Hand asked abrasively.

"Simmons," Coulson asked, "My team needs her."

"I'll have Agent Triplett send her over," Hand acknowledged, "Send me your coordinates."

"We're on our way to Istanbul," Coulson answered, "I'll have Skye send our position to Triplett."

"Coulson," Hand began warily, "I know you guys like to do your own thing, but that case was closed for a reason, and it's not just because S.H.I.E.L.D. didn't find anything, several agents died on that case, Fury decided that it wasn't worth the risk, besides Cole got the package back."

"I don't know if you've noticed, Victoria," Coulson answered slyly, "But we're not exactly S.H.I.E.L.D. anymore, are we?"

"No," Hand said, "I suppose we're-"

Her end was cut off, Coulson only saw static from his office.

"Agent Hand?" Coulson yelled, "Victoria, what happened? SKYE!" Coulson shouted out to the 'hacktavist', "I lost the Hub, I need you to get it back for me, Simmons could be in danger!"

"I'm on it," Skye came rushing in and went to work on Coulson's computer, "I'll see what I can do."

* * *

**Istanbul, Turkey,**

**3 Hours after the death of Thomas Nash,**

**1 Hour after the disbanding of S.H.I.E.L.D.**

"Well, Agent Garrett," A man in white shirt with Black lightning Bolt, stood over the former S.H.I.E.L.D. agent, brandishing a gun down at him, "We meet again, don't we."

"You're not going to get away with this," Garrett threatened idly, "S.H.I.E.L.D. will find you, and they will make sure everybody knows the true identity of the Broker."

"I don't know if you heard," He said, "But Nick Fury is dead, and I have it on good authority that you didn't work him."

"Guilty as charged," Garrett smiled, thinking the Broker was his ally.

"What is it you guys always say?" The Broker asked thoughtfully.

"Cut off one head, two more will take it's place," Garrett said, realizing that his life was about to come to an end, "Hail Hydra."

BANG, the shot rang out through the empty alleyway, and one red drop fell from Garrett's forehead.

"Well then," the Broker nealt down and taped something to the dead, "I think Philip would like to see this," he took a picture and left the alleyway.

* * *

**The Bus,**

**2 Hours Away from Istanbul,**

**3 Hours after the death of Thomas Nash,**

**1 Hour after the disbanding of S.H.I.E.L.D.**

"AC," Skye came in and addressed Coulson on the problem he had asked her to fix, "I couldn't fix the problem, but I can tell you that somebody in between is disrupting the connection, it wasn't on the Hub's end. This person is using Rising Tide techniques, and I'm going out on a limb here but I think it's the Broker-" She stopped as soon as she saw the image on the large screen, she stopped talking, "Is that…"

"Yes," Ward said, attempting to conceal his true feelings through a mask of emotionlessness.

The image in question was a picture of Garrett's dead body with a piece of paper that read "Would the next two heads please stand up?"

"Where did you get this image?" Skye asked, looking more closely to find any clues as to the location.

"The Broker," Ward said, "He's telling us that he knows we're on to him, as well as showing us that he's not working with Hydra. Or at least he wants us to think that."

"The Broker has bases all over the world," Coulson said, "But Garrett was assigned to go to Istanbul to save a hostage. So we believe that's where this image was taken. The Broker has something with Istanbul, possibly some piece of history that connects him to that city."

"Coulson," Fitz came in at a slight jog, "What's the situation with Jemma?"

"I spoke with Victoria Hand," Coulson addressed the young scientist, "She's sending Simmons over to the Bus with Agent Triplett, she'll be here in a few hours."

"Oh no," Fitz said darkly, his face went white, "Oh no, we have to go to the Hub now!"

* * *

**Istanbul**

**3 Days after the Death of Thomas Nash,**

**3 Days after the disbanding of S.H.I.E.L.D.**

"Ward!" Skye shouted at her SO, "I'm going out to get some coffee," She was standing just outside the bus, which had been stationed at a guarded runway, covertly hidden inside the bustling Turkish city, "Do you want anything?"

"Yeah," He said, cleaning his weapon, "I'll have just a large black coffee."

"See ya," Skye said, then looked back, "I'm sorry about Triplett, Ward. I know he was your friend. Tell Coulson and May I'll be back in twenty minutes."

"Will do."

Skye quietly moved through the streets till she found a small shop where she didn't think anyone would look for her. Throughout her career as a hacktavist, as she liked to put it, she had learned to move through places, both large and small, populated and unpopulated, without being detected, this would come in handy for whatever she and her team would do next.

She paid for her friend's coffee and left, Miles' million bucks was coming in handy.

"Oof," She was jolted out of her thoughts as she bumped into a local. It was a man, he wore a clean white t-shirt with a Black lightning Bolt on it.

"Üzgünüm," The man said something in a thick turkish accent, but she didn't understand it, so she kept walking. What she didn't notice was that the man was following her, he was also walking at a brisker pace, and right as he caught up to her on an abandoned street, he put a bag on her head, and shoved her into a van.

* * *

**Base of the Broker,**

**Location Unknown**

**3 Days after the Death of Thomas Nash,**

**3 Days after the disbanding of S.H.I.E.L.D.**

The Bag was lifted off of Skye's head, but she still couldn't see anything, she was in a dark room, no windows for light to creep through. It could have been just larger enough for her, or it could have been as large as the Hub, she had no way of knowing.

"Ward!" Skye shouted to empty darkness, "GRANT! WHERE ARE YOU!" She was tied to a chair, she wasn't gagged or blindfolded, "Where are you? Coulson? Simmons? Fitz? MAY!?"

"They can't hear you," A voice came out of the darkness, "Only I can."

"Who are you?" Skye, for the first time in years, was willing to admit that she was terrified.

"Oh, I am the Broker," The man said, it was the same man from the coffee shop, she could only this time, there was no accent, "And you have a piece of information that I want, Skye."

**NEXT: The Secret of the Rising Tide!**

* * *

**A/N: **Alright! I have officially dropped one hint as to who Skye's parents are, it's in this chapter but I won't tell you where. Also if you get the hint, please don't spoil it by putting it in a review, if you have a theory based on the hint, you can pm, and I may confirm it or not, I haven't decided yet. Anyway I hope you liked it, and I promise you that there will be Fitzsimmons in the coming chapters.


	3. Chapter 3: The Tide Has Risen

**A/N: **As the title suggests this chapter delves into the secret of the Rising Tide. It will not reveal it, but it does begin to unravel the secret of it's existence and why Skye was drawn to it. And I don't know if you've heard yet, but Agents of S.H.I.E.L.D. is getting a second season, and Agent Carter is going to be a full series on ABC, also this fall, so I can't wait for both of those! Can you guys believe that there are going to be FIVE new comic book shows this fall? Because I can't!

* * *

**A War In Secret**

**Chapter 3: The Tide Has Risen  
****The Bus,  
****2 Hours Away from Istanbul,  
****3 Hours after the death of Thomas Nash,  
****1 Hour after the disbanding of S.H.I.E.L.D.**

"Oh no," Fitz said darkly, his face went white, "Oh no, we have to go to the Hub now!"

"What's wrong Fitz?" Ward was confused, but he had a sneaking suspicion he knew the answer already.

"Triplett," the rocket scientist said, biting his lip, simultaneously pulling up footage on the monitor, "He's Hydra! The man Agent Hand sent Simmons with is Hydra! Simmons, is going to die, or worse, she could be tortured, and brainwashed into working for Hydra! We have to save her!"

"Skye," Coulson turned to the young hacker, "I need to get into S.H.I.E.L.D.'s flight manifest and plain controls. Find out where Trip and Simmons are and make sure May knows so we can intercept them as soon as possible," He turned back to Fitz, "We're going to get her back, Leo, and we'll make Triplett pay for what he's done," He nodded at Ward and had him move Fitz down to the lab to occupy him.

"You know I never thought I'd see a black Nazi," Skye said in an offhanded comment. She received raised eyebrows from both May and Coulson, "What? It's something to think about."

"Hydra isn't a Nazi organization anymore," Coulson said, "And based upon a conversation I had with Cap, I don't think it ever really was. Johann Schmidt created Hydra under Hitler because he gave Schmidt funding. But Schmidt only worshipped himself as a god, he didn't care about Hitler's Aryan beliefs, he just wanted soldiers to acknowledge his craved godhood. He'd take anything he could get. I don't know why Trip joined Hydra, but it's probably like a 'Divine Demonstration' or something to that effect," He sighed and began walking over to his office, "Skye, find Trip's plane, and May try Fury again, we need to find him."

* * *

**Base of the Broker,  
****Location Unknown,  
****3 Days after the Death of Thomas Nash,  
****3 Days after the disbanding of S.H.I.E.L.D.**

"So, you're the Broker," Skye said feigning confidence she may never have again, "The big bad Broker wants some hacker that joined S.H.I.E.L.D., I'm pretty sure we can both agree that I'm useless to you, right? I mean there's nothing special about me."

"Oh, quite to the contrary Ms. Amequelin," He answered, fiddling with something on a table, "You are very special, quite possibly the most special woman in the universe. If you weren't special, then why would S.H.I.E.L.D. hide your heritage from you and the world? Why would the deputy director of S.H.I.E.L.D. die protecting you from the world? My dear you have the potential to change the world, whether for better or for worse. And I want to help you fix the world, I want to help you save the universe. Why else would I have created the Rising Tide?"

"You created the Rising Tide," the revelation made Skye's face unnaturally pale, "But why? Because you want the world to be a better place, a place where there are no dirty secrets?"

"What? No!" He said taken aback that she would even think that, "I make my living off of secrets, I wouldn't have a job without them. No, I created the Rising Tide, well partly to be a pain S.H.I.E.L.D.'s ass, but also to keep tabs on you, I needed to know where you were, because I knew you believed in that no secrets crap!"

"You… You're mad," Skye said, staring at him in fear, but also registering the reality of the situation, "But I apparently have something you want, you have something I want, so… let's make a deal."

"You would betray your friends for information on your parents," He said, smiling wickedly at her, "You would give up your family for information. You are a very selfish girl."

"Desperate times call for desperate measures," Skye said, keeping a cool head.

"I suppose you're right."

* * *

**The Bus,  
****Istanbul,  
****3 Days after the Death of Thomas Nash,  
****3 Days after the disbanding of S.H.I.E.L.D.**

"Hey, Coulson," Ward walked up into the living room of the plane, "Have you seen Skye?"

"No, have you checked her bunk?" Coulson answered focusing on the turkish newspaper, "She's probably in there on her computer."

"No, I checked," Ward said, still standing there, worrying, "She went out to get coffee about four hours ago, and hasn't returned, or even sent us a message."

"There's a GPS tracking chip on her phone," Coulson said, standing up, "I'll get Fitzsimmons to run a trace for it. Find out where she is, I'm sure she's fine, Ward. I'll go down right now."

"I'll come with you," Ward said, refusing to remain calm.

"Ward," Coulson said looking at the exhausted man, "You need to get some sleep, I don't think you've slept since Skye was shot by Quinn."

"I'll sleep when we're all on this plane together," Ward said firmly.

"Coulson," Simmons greeted the two men as they descended the stairs into the lab, "I wasn't expecting you for another hour, is something wrong?"

"We can't find, Skye," Ward spoke up immediately, "She went into the city, but she hasn't responded to any of my texts or calls."

Simmons looked nervously from Ward to Coulson

"Ward would feel better if you activated the tracer in her phone and found out where she is," Coulson said in a maddeningly calm voice.

"I'll get right on that," Simmons said moving over to the holo-table, "Fitz! Could you help me with the tracer on Skye's phone?"

"Yeah, sure," Fitz said offhandedly, "It'll take a couple of minutes, so be patient."

* * *

**S.H.I.E.L.D. Small Transport 5732,  
****Approximately 4 Minutes from the Bus,  
****3 Hours after the death of Thomas Nash,  
****1 Hour after the disbanding of S.H.I.E.L.D.**

"So, Trip," Jemma asked nervously, "Where are you going after you drop me off at the bus?"

"I… I don't know," He answered, wiping the sweat off of his forehead, "Garrett is going to kill me."

"Why would he do that?" every piece was sliding into place for her.

"Because I'm supposed to kill you," He said turning away from the controls, and standing up.

"You don't have to do this Antoine," Jemma said, shrinking back into her chair, Trip standing over her, "You don't have to be the bad guy, you can fix this!"

"No," Antoine said, "I don't, which is why-"

BOOM! Several shots rang out a few hitting the plane, forcing Triplett to fall to the floor.

* * *

**The Bus,  
****Approximately 2 Hours Away From Istanbul,  
****3 Hours after the death of Thomas Nash,  
****1 Hour after the disbanding of S.H.I.E.L.D.**

"Coulson!" May's shout rang out through the entire Bus, "We're taking fire from unknown sources. I recommend you all strap in!"

"Copy that," Ward said, buckling himself in the living area.

"Coulson!" Skye said moving towards Ward and Phil, "I have the coordinates of the plane, "It's right above us."

"Is it one of the plane's shooting at us?" Coulson asked, rather angrily.

"No," Skye responded looking at her tablet screen, "I think those planes are targeting both us and Triplett."

"Agent Coulson," Antoine Triplett's face appeared on the holo-monitor, "I think we should make a deal."

**NEXT: AGENTS OF S.W.O.R.D.!**

* * *

**A/N: **So I have about 30 chapters and an Epilogue planned out, and I could go farther with a sequel, basically what I'm saying is there's a lot I can do with this story. And I will tell you now that the Avengers are probably going to make an appearance in Chapter 8. I may also, in a sequel, expand the universe to include Spider-Man, the FF and the X-Men. Anyway as always leave a review, I wasn't particularly comfortable with the conversation about Hydra, I just thought I didn't execute it very well, maybe I'm wrong who knows, and if you have any theories about Skye's parents or anything feel free to PM me! And I almost forgot. Hail Hydra and SIX SEASONS AND A MOVIE!


	4. Chapter 4: Broken

**A/N: **I hope you liked the last chapter, we're really getting into the meat of the story here, and I'm laying the groundwork for something I think is pretty cool, and really hope you like it!

* * *

**A War In Secret**

**Chapter 4: Broken**

**Melbourne International Airport  
****28 Miles From Cape Canaveral, Florida  
****14 Hours after the death of Thomas Nash,  
****12 Hours after the disbanding of S.H.I.E.L.D.**

"Last call for boarding flight 23578 to Houston, Texas," A voice said over the airport intercom, "First Class boarding will now begin for flight 23649 to Philadelphia, Pennsylvania."

"Excuse me ma'am," A caucasian male with dark hair that hung loosely off his head, "Where is the baggage claim for flight 23486 from Istanbul?"

"Ah, yes, you'll be wanting to go to baggage claim 3B," the cute, perky blonde airport hostess answered with the obligatory smile.

"Thank you very much," He said, leaving without waiting for an answer.

He walked over to the escalator, looking to see if any cameras could find him. He detected four security cameras, pulled out his phone and pressed several keys.

He waited for a few minutes and grabbed his two black duffle bags and left. he walked past the security kiosk, gave the pudgy officer a kind smile, and continued to walk.

"Excuse me, sir," The officer walked over to him, "Could you please tell me what your business in Florida is?"

"Yes, of course," He said stopping, and facing the kiosk, "I have some business in Cape Canaveral. I'm doing some work for NASA."

"Of course," he said, looked at his clipboard, and said, "I'm sorry could you please step in here, I need to check your bags."

"Anything I can do to help the TSA," He said, stepping in behind the officer. Two minutes later he walked out of the room without the officer.

* * *

**The Bus,  
****Istanbul,  
****3 Days after the Death of Thomas Nash,  
****3 Days after the disbanding of S.H.I.E.L.D.**

"Alright, I've got the coordinates, switching to street-view for you," Fitz said, "Skye taught me some tricks, isn't she so cool! I love that she's one the Bus with us," Jemma gave him a stare, "As I do all of you too."

"FITZ!" Ward shouted, "We need to see where she is! I need to she's okay!"

"Sorry," he said, stopping his smile short, "And here it is, the address in street-view for you. Oh," a warehouse on the outskirts of Istanbul was shown on the large computer, "That's probably not good. Right?"

"Ward," Coulson looked up at the taller man, "I owe you an apology. Sorry."

"Thank you," Ward said, "Apology accepted. Now we need to suit up and go get her!"

"Right," Coulson trotted out, Ward following into cargo bay, "May, I need you down here. We think Skye's been kidnapped, you, Ward and I are going to get her out of there. That's priority one, priority two is getting this bastard."

"It's probably the Broker," May climbed down the stairs at lightning speed, "He's been baiting us for three days. He's wanted something from us, and this almost definitely what he wants."

"So this is a trap?" Ward asked.

"Of course it is," Coulson answered, "But we need to bring this guy in alive, he's been a thorn in S.H.I.E.L.D.'s side for almost nine years, he has leaked hundreds of S.H.I.E.L.D. operations, and he killed Quentin Cole."

"We don't know that he killed Cole," Ward said.

"He was one of the best agents S.H.I.E.L.D. has ever had," Coulson said, loading his pistol, "Only someone who knew all of S.H.I.E.L.D's intel could have gotten him."

"He was an ass," May muttered.

"Whatever your opinion on him, May," Coulson retorted, "But he was a very good agent."

"Let's just get this over with," May said, glaring at Coulson.

* * *

**The Bus,  
****Approximately 2 Hours Away From Istanbul,  
****3 Hours after the death of Thomas Nash,  
****1 Hour after the disbanding of S.H.I.E.L.D.**

"Agent Coulson," Antoine Triplett's face appeared on the holo-monitor, "I think we should make a deal."

"What do you want Triplett!" Coulson shouted.

"If I can dock on the Bus," Triplett said, "I can hand over Simmons to your team. I don't need anything in return, only her safety."

"MAY!" Coulson shouted, "I NEED YOU TO PREPARE THE BUS FOR TRIPLETT TO DOCK!"

"What the hell Coulson!" Fitz yelled, in his scottish accent, "What do you think you're doing!"

"I'm saving Simmons' life," Coulson responded, "Now go get Ward! I need him for the extraction!"

"I'm here," Ward said struggling to move into the cabin, "What do you need?"

"I need you to get Simmons from Triplett's plane," Coulson said, "He'll be docking any second!"

There was a large shock, as the small plane landed on top of the Bus. The cargo bay hold on top opened revealing the frightened British girl.

"Jump down!" Ward shouted, "I'll catch you! Don't worry, you'll be fine!"

Simmons jumped down, and as she was mere centimeters from Ward's arms, there was a boom as Triplett's plane exploded, hole was blown open on the top of the plane, and the pressure completely flipped, sucking both Ward and Simmons out of the plane.

* * *

**The Peak,  
****In The Earth's Orbit,  
****1 Day after the death of Thomas Nash,  
****1 Day after the disbanding of S.H.I.E.L.D.**

"Agent Brand," A female in a green combat suit approached her superior, "The last shuttle has arrived."

"Thank you," the green haired woman turned to the agent, "Bring them to the prisoner, I want a full detail 24/7 on her, she is our first priority."

"Yes, Ma'am," She said bowing out, turning and directing the new agents to the cell.

Boom! Boom! Boom! The station shook as female warrior in red and white viking armor charged at the female agents. Agent Brand drew her gun and shot at the warrior, but she dodged the shots and knocked Brand down, drawing a double-bladed sword.

"Where is the Seductress!" The warrior shouted, pinning the agent down, "Where have you taken Lorelei! Tell me or I kill your superior officer!"

"Down the hall to the right!" One of the agents said, and the warrior took off running.

* * *

**Base of the Broker,  
****A Warehouse in Istanbul, Turkey,  
****3 Days after the Death of Thomas Nash,  
****3 Days after the disbanding of S.H.I.E.L.D.**

"Desperate times call for desperate measures," Skye said, keeping a cool head.

"I suppose you're right." The Broker said smiling.

"What do you want from me?" Skye asked.

"I need you to lie down on this bed," He pointed to a small cot, "I need to do a small operation, the pain will not be great, I can put you under an anesthetic if you would like."

"I'd like that yes," She said, taking a large gamble, "What operation are you doing?"

"I'm taking a bone marrow sample," He said calmly, "I need to test a theory, to make sure my hypothesis is correct."

"I see," Skye lay down on the bed.

"Alright," He said standing over her, "I need to inject this into your bloodstream, it's a simple anesthetic, there will be a small prick."

"Ouch," She involuntarily screeched, "Sorry."

"That's quite alright," He said with a genuine smile, as he pulled a mask over her face, "This is pure Oxygen, it will help you stabilize your blood pressure, while I put you under."

"Alright," Skye said through the mask, "It feels very artificial, the air I mean. It's like breathing in flavored paper."

"Ha," He chuckled, then turning to her, "I'm going to need you to count backwards from ten, alright?"

"Yes," She said, "Ten, Nine, Eight, Seve…" She trailed off and fell into a dreamless sleep.

* * *

It was half an hour later, and the Broker was bottling the sample of the girl's bone marrow. There was a boom as smoke filled the room and three people were aiming guns at him.

"Hello, Philip," He said with a slight smile, "I had hoped you would come a little bit later. Oh well."

"You son of a bitch!" Coulson yelled, charging at him and throwing a punch, knocking the Broker down.

"Do you know him?" Ward said, picking Skye up off the bed, carrying her bridal style.

"Yes," May said sternly glaring at the broker, getting up from the floor.

"I do think that was a bit of an overreaction," He said standing up, "But I suppose you are rather angry at me. All things considered."

**NEXT: SIF VS. LORELEI & THE BROKER REVEALED!**

* * *

**A/N: **I will tell you now that the Broker is a huge character in this story, as is Sif**. **I hope you liked this chapter, and as always Hail Hydra & SIX SEASONS AND A MOVIE!


	5. Chapter 5: World of Secrets

**A War In Secret**

**Chapter 5: World of Secrets**

**The Air Above the Bus,  
****2 Hours Away From Istanbul,  
****3 Hours after the death of Thomas Nash,  
****1 Hour after the disbanding of S.H.I.E.L.D.**

"Jump down!" Ward shouted, "I'll catch you! Don't worry, you'll be fine!"

Simmons jumped down, and as she was mere centimeters from Ward's arms, there was a boom as Triplett's plane exploded, hole was blown open on the top of the plane, and the pressure completely flipped, sucking both Ward and Simmons out of the plane.

"SIMMONS!" Ward shouted, flailing in the air, desperately trying to find his friend in the shower of bullets, "Where are you?"

There was a sudden burst of air, as a dark figure with wings flew into the battle, and hoisted Ward over the battle, and towards the falling scientist.

"Who are you?" Ward said, staring up at his winged savior, "Please tell me you're not an angel, I really can't deal with more cosmic shit right now."

"Don't worry, I'm not an angel," He replied, smiling sadly, "My name is Sam Wilson, I'm a friend of Captain America. Agent Hand told me there was a loyal S.H.I.E.L.D. team was in trouble."

"Ward!" Simmons shouted with relief as she was caught by Sam Wilson, "What happened?"

"I'll tell you in a moment," Ward said.

"Hold on to your lunches!" Sam shouted, "We're gonna do a flip in mid-air," Sam made an adept move as he he flipped over in mid-air and dropped the agents in the plane.

"MAY!" Coulson shouted, "GET THE PLANE DOWN TO THE NEAREST STRIP OF LAND! NOW!"

The Plane descended into Wales, as the plane crashed into an empty Welsh field.

"Are we all alive?" Skye asked, nearly out of breath, "Are we all here?"

"Yeah, we're alive," Coulson said falling over onto the plane's floor, "And we're here too."

* * *

**The Bus,  
****Istanbul, Turkey,  
****3 Days after the Death of Thomas Nash,  
****3 Days after the disbanding of S.H.I.E.L.D.**

Coulson lead the Broker into the bus, with May holding a gun to his head and Ward carrying Skye, bridal style.

"YOU GUYS ARE ALIVE!" Simmons shouted, seeing her friends.

"Agent Jemma Simmons," The Broker smiled, "How's your father? Have you talked to him recently?" He looked psuedo-innocently at her, she stared at him stunned, and scared, "That's what I thought."

"Don't you dare look at her!" Leo shouted at him.

"Agent Leo Fitz," The Broker smiled, "How is your brother? Quite the brilliant scientist, don't you agree? Oh I forgot what happened Edinborough, I feel so bad for bringing that up."

"Close your mouth and keep moving," May ordered, hitting him over the head.

"That was quite mean," The Broker said, turning around and looking at her.

"Get him to the interrogation room," Coulson ordered, "Ward, get Skye to the medical I want to know what he did to her," Ward nodded then moved off to the medical bay.

May pushed the broker forward, and walked him toward the interrogation, and sat him down and cuffed him to the table.

"Nothing?" May said, "You just tortured a young, innocent, good woman, and you have nothing to say for yourself?"

"I stand by my actions, Melinda," He replied, "I know you don't like me, and you have every right to do so, I was an ass to you, and I apologize to you for it. But what I did was for the betterment of all humanity."

"I'd like to hear a better explanation," Coulson said, walking into the room, with a few files and sitting down, "You can leave now May, I'll take it from here," May nodded and left closing the door, "Quentin Cole, I thought you were my friend, I thought you died, we mourned for you! And all you've been doing for the past nine years, is killing S.H.I.E.L.D. agents. And you explain your actions by saying you're trying to save humanity? What are you really doing? What are you trying to prevent?"

"Evolution," Quentin replied with a somber face, "Everything dies, it is the natural course of things, all species evolve, and eventually all things, all beings become obsolete, and I accept it. It is the unnatural acceleration of that end that I do not tolerate, and that is what I'm working on preventing."

"What does this have to do with Skye?" Coulson asked.

"Oh, everything, the girl has to do with everything," Quentin said raising his arms as far as the cuffs would allow, "You're not alone anymore, and you never really were."

* * *

**The Peak,  
****In The Earth's Orbit,  
****1 Day after the death of Thomas Nash,  
****1 Day after the disbanding of S.H.I.E.L.D.**

"Lorelei!" Sif shouted, "Your place is a cell in Asgard! Not a suite in Midgard!"

"Oh, my dear Lady Sif," Lorelei replied, seductively, "I think you have more trouble than just me."

Four fully armored soldiers attacked Sif, firing off several rounds at the female warrior. She dodged the bullets, and swung her sword disarming the agents. Disarmed, the soldiers charged at her, but with her superior strength and skill, Sif easily knocked the soldiers. Lorelei charged at her combatant, drawing her own sword, and began fighting.

She pushed back Sif into the hallway, and descended into a room filled only with a dark haired man toiling away on large monitor.

"I'm sorry, ladies," He said turning to them, watching Lorelei tackle Sif, "But I really need some privacy…," He paused, mouth agape, "Holy shit, you are the most beautiful woman I have ever seen."

"Thank you," Lorelei said, "I have been told that before, now if you please, could you kill my enemy."

"Sorry, red," He said smiling, "I've always had more of a thing for brunettes," He flung a small projectile at the seductress and she crumpled, "I do apologize, but if you please, I'd like there to be no record of my ever being here."

"Who are you?" Sif asked, dumbstruck by what an apparent mortal had just been able to do.

"My name is Quentin Cole," He said smiling, "And I meant what I said about your beauty, I do hope we meet again soon, Lady Sif," And with that he left the room, and once he was out of earshot of the warrior, he pulled out a small recording device, "Broker Log Entry #7312. I found them, they're preparing for the genesis. Next objective, find the girl, make positive identification, prepare for and prevent the first of many genetic wars."

* * *

**The Bus,  
****Istanbul, Turkey,  
****3 Days after the death of Thomas Nash,  
****3 Days after the disbanding of S.H.I.E.L.D.,**

"What do you know, that we don't Quentin," Coulson shouted, smacking the table with both hands.

"Isn't that a bit cliche?" Quentin asked. Coulson raised his eyebrow, "You know, the whole 'smacking your hands on the table' thing. I mean it's like we're watching a 'Law & Order' repeat."

"Well, you are a homicidal sociopath," Coulson sitting down.

"I take offense to that!" He replied pointing a finger at his interrogator.

"You were supposed to," Coulson said, "You were my friend, I stood up for you in front of other agents, they hated you, and I defended you."

"I never asked you to do that," he answered.

"You say you're fighting for humanity?" Quentin nodded, "Then who are you fighting against? Hydra? Asgard? Loki? The Chitauri?"

"You wouldn't believe me if I told you," Cole answered solemnly.

"Try me."

"A secret race of evolved beings who live on the moon."

**NEXT: A SECRET RACE OF EVOLVED BEINGS WHO LIVE ON THE MOON!**

* * *

**A/N: **So, that happened. Skye will be very important to the overall story, and the Broker is Quentin Cole, and Sif is here! There are a lot of unanswered questions between Coulson and Cole, and they will begin to unravel starting next chapter! So please review! Hail Hydra & SIX SEASONS AND A MOVIE!


End file.
